k-meech/registrationtree

registrationtree's Issues

Latest versions of elastix error on Windows

Elastix versions greater than 5.0.0 cause errors on windows

Crop mangement

• better management of crops
• save and re-use crops
• save into metadata

Give option to use absolute path in xml saved from registration

Relative paths are currently used for the saved xml from registration plugin. This means that if files are moved around (and not as a whole folder structure), the paths break.

It would be good to provide some checkbox to save as relative vs absolute

Image brightness and contrast in new bigwarp version

Brightness and contrast of images are off when loaded in the newest bigwarp version.

(can be adjusted via top menu of bdv window manually - but not via the side panel)

Disable the auto writing of the initial and transformed images

This should be a tickbox option in the elastix menu, rather than on by default.

Export functionality

• export images in fixed or moving space (to tiff)
• export images in fixed or moving space by writing xml with required transforms (for bdv style stuff)

Get manual transforms working

• try to re-use code in bdv playground
• pop up orthogonal views for this too

Elastix

• get elastix working after previous transform
• PRs to elastix repo

Using different masks in a row aren't written

When a mask is written, it just checks if a certain name already exists - which for a fixed mask is always 'FIXED_MASK_0' or something like this. Therefore, if you use a new mask for the next registration, it will just re-use the old one as that filename already exists. Need to give some unique name somehow / some way to specify which file it came from.
(at the moment, just wipe the folder in between successive masks)

8-bit hdf5 images are converted wrongly on writing for elastix

At the moment, hdf5 images are read with 16-bit imageloaders in bigdataviewer - see: bigdataviewer/bigdataviewer-core#128

This gives weird results, as I then try and convert from 16-bit to 8-bit to write for elastix and end up writing images to a strange range. Would be easiest to fix upstream.
Use n5 for now.

Downsampling choices

-save in metadata

• display the image size to write, and ideally a predicted size in GB
• Ideally we allow them to screen too e.g. you write, open in imagej, then they say it's good or not and can choose a different scale

View space

• Get switching view space working

Name Sources by transform

• look at wrapping as named sources like BigWarpInit does

Save xml from registration plugin doesn't allow filename to be added on mac

The file dialog for this is currently an 'open', rather than a 'save'. On mac, this seems to mean you can't give an extra filename.

Swap to a save dialog